microRNA Target Prediction Tools

microRNA Target Prediction Tools

miRecords
is resource for animal miRNA-target interactions developed at the
University of Minnesota. miRecords consists of two components. The Validated Targets
component is a large, high-quality database of experimentally validated
miRNA targets resulting from meticulous literature curation. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs

PicTar
is an algorithm for the identification of microRNA targets. This
searchable website provides details (3′ UTR alignments with predicted
sites, links to various public databases etc) regarding microRNA target
predictions in vertebrates, several Drosophila species, and C. elegans.

miRanda
is an algorithm for finding genomic targets for microRNAs. This
algorithm has been written in C and is available as an open-source
method under the GPL. MiRanda was developed at the Computational Biology
Center of Memorial Sloan-Kettering Cancer Center. This software will be
further developed under the open source model, coordinated by Anton
Enright and Chris Sander (miranda@cbio.mskcc.org).

TargetScan: Prediction of microRNA targets
– These are the most recent TargetScanS predictions (April 2005). They
are essentially the 3′UTR targets reported in the Lewis et al., 2005
paper, with a few changes arising from updated gene boundary definitions
from the April 2005 UCSC genome browser mapping of RefSeq mRNAs to the
hg17 human genome assembly. To avoid difficulties in browser display,
the few predictions spanning splice junctions are excluded.

RNAhybrid
is a tool for finding the minimum free energy hybridization of a long
and a short RNA. The hybridization is performed in a kind of domain
mode, ie. the short sequence is hybridized to the best fitting part of
the long one. The tool is primarily meant as a means for microRNA target
prediction.

miRNA – Target Gene Prediction at EMBL
– This website provides access to our 2003 and 2005 miRNA-Target
predictions for Drosophila miRNAs. Both methods make use of genome
comparison across insect species. Our 2005 predictions are based on
pairing rules from a systematic experimental study (Brennecke &
Stark et al., 2005) and have a very high sensitivity and specificity as
assessed by experimental tests (see Supplement in Stark & Brennecke
et al., 2005). We thus highly recommend to use the new predictions.

RegRNA
– is an integrated web server for identifying the homologs of
Regulatory RNA motifs and elements against an input mRNA sequence. Both
sequence homologs or structural homologs of regulatory RNA motifs can be
identified.

psRNATarget: A Plant Small RNA Target Analysis Server
– A plant small RNA (including microRNAs) target analysis server, which
features two important analysis functions: 1) reverse complementary
matching between miRNA and target transcript using a proven scoring
schema, and 2) target site accessibility evaluation by calculating
unpaired energy (UPE) required to “open” secondary structure around
miRNA’s target site on mRNA. PsRNATarget incorporates recent discoveries
in plant miRNA target recognition, e.g. it distinguishes translational
and post-transcriptional inhibition, and it reports the number of
miRNA/target site pairs that may affect miRNA binding activity to target
transcript. psRNA Target is replacing miRU (Plant microRNA Potential
Target Finder) by the same group.